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The four-time champion German, who finished second behind Red Bull’s Max Verstappen in the Mexican Grand Prix, said he wanted to win another title by beating the best opposition.
The Ferrari ace was reported to the stewards for not slowing sufficiently when the rain-hit opening practice was red-flagged after Charles Leclerc had brought gravel back on the circuit.
Valtteri Bottas held off Max Verstappen to take second almost 13 seconds behind Hamilton in a breathless 53-lap race at the fast-flowing Japanese circuit.
'Never in a million years': Lewis Hamilton grabs 80th pole at Japanese Grand Prix as Sebastian Vettel flounders
Vettel skidded off twice in his desperation to set a time and his starting position of eighth will be his lowest of a season which began so brightly but looks like ending in bitter disappointment.
Vettel denied that Ferrari has consistently had the better car, insisting the difference between them and Mercedes has been minimal.
It was Hamilton's third win in Russia, his fifth in six races and the 70th of his career, confirming he has the momentum to clinch a fifth title triumph with five races remaining.
Sebastian Vettel was hardly a jovial figure when he arrived in Singapore, but he was incandescent after Ferrari's weekend unravelled.
Ferrari have had the faster car than the Mercedes of late but they have failed to come up with the consistency required to win titles.
The four-time champion German admitted that he felt he and his team had let down Ferrari's passionate tifosi by failing to win after locking out the front row of the grid.
Lewis Hamilton waited until the end of lap 28 to come in for fresh tires, handing the lead to Bottas who was ahead of a charging Raikkonen.
The German clocked a best lap of one minute and 21.105 seconds to outstrip the Finn by two-tenths of a second at the high-speed Autodromo Nazionale.
Sebastian Vettel can close the gap, or even overhaul it, when he takes on championship leader Lewis Hamilton again this weekend in what should be a supercharged Italian Grand Prix.
Hamilton, who started from a Belgian record fifth pole position, came home a well-beaten second for Mercedes, having been unable to threaten his German rival.
The defending world champion came home 17.123 seconds ahead of title rival and fellow four-time champion Sebastian Vettel of Ferrari.
Vettel was out-qualified by Ferrari team-mate Kimi Raikkonen for only the third time this year, but the Finn was also not happy.